From a45498150a419d1e3a0fd8814e13793cdc5f7412 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 18 Aug 2011 11:18:29 -0400 Subject: [PATCH] Remove non-ascii char --- .../sting/gatk/walkers/indels/RealignerTargetCreator.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index 08ed1af52..145d0327c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java @@ -57,7 +57,7 @@ import java.util.List; *

* The local realignment tool is designed to consume one or more BAM files and to locally realign reads such that the number of mismatching bases * is minimized across all the reads. In general, a large percent of regions requiring local realignment are due to the presence of an insertion - * or deletion (indels) in the individualÕs genome with respect to the reference genome. Such alignment artifacts result in many bases mismatching + * or deletion (indels) in the individual's genome with respect to the reference genome. Such alignment artifacts result in many bases mismatching * the reference near the misalignment, which are easily mistaken as SNPs. Moreover, since read mapping algorithms operate on each read independently, * it is impossible to place reads on the reference genome such at mismatches are minimized across all reads. Consequently, even when some reads are * correctly mapped with indels, reads covering the indel near just the start or end of the read are often incorrectly mapped with respect the true indel,